#!/usr/local/bin/perl -w
###############################################################################
#              Mike Galsworthy's "Free Text to MeSH" converter                #
#                                                                             #
#                                                                             #
#          PROGRAM 1 :  Retrieving PubMed articles in Medline format          #
#                                                                             #
#     (credit to Oleg Khovayko for key Medline download parts of script)      #
#                                                                             #
#                                                                             #
###############################################################################


#### PART 1. SETTING COMMAND-LINE TERMS #######################################

use Getopt::Long;

my ($term, $keep, $retmax);

GetOptions ("query:s" => \$term, "records=i" => \$keep, "batch=i" => \$retmax);

if (!($term)) {
    die "No query term given. Use the --query 'term here' option.\n";
    }

#### PART 2. E-SEARCH ON THE QUERY TERM (USING "HISTORY") #####################

use LWP::Simple;

$base = "http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?".
        "db=Pubmed".     "&".
        "retmax=100".    "&".
        "usehistory=y".  "&".
        "term=";

$signature = '&tool=bitola_medsum&email=mike_galsworthy@yahoo.co.uk';

$esearch = get($base . $term . $signature);

$esearch =~
m|<Count>(\d+)</Count>.*<QueryKey>(\d+)</QueryKey>.*<WebEnv>(\S+)</WebEnv>|s;

my $Count    = $1;
my $QueryKey = $2;
my $WebEnv   = $3;

print '<font size="3" face="Times">';
print "Your query is: $term\n <br>";
print "And it found $Count results\n <br>";
if ($Count<1501) {
    print "Yes, I can PROFILE that in one go.";
    print "\n <br>";
    }

if ($Count>1500) {
    print "NOTE: That will take too long for one PROFILE summary - I can only process 1500 at a time.\n <br>";
    print "Please modify your query, or run several queries and with each: ";
    print "<a href='javascript:onClick=alert(\"To limit by year: simply add 2007[dp] to your query to get the year 2007 only, or add 2006:2007[dp] to get the years 2006 to 2007\")'>limit by year</a>";
   print ". <br> However, if you want to run Timeline, the number of records is not a limiting factor.\n <br>";
    }